IMAP-WORKFLOWS

Snakemake workflows for microbiome and multi-omics data analysis

Fostering Reproducible Microbiome data Analysis with Snakemake workflow

Microbiome and multi-omics snakemake workflows

General overview

The workflows displayed in this document define the snakemake rules in a DAG (directed acyclic graph) format. You may find a link to the interactive snakemake HTML report in some workflow. The link will enable you to explore the workflow and associated statistics. While exploring the interactive workflow, you can close the left bar (the overlap) to get a more expansive display view.

IMAP-PART 01

Software requirement for microbiome data analysis

Explore the IMAP-PART 01 interactive snakemake report (if available) here.

IMAP-PART 02

Exploring and profiling SRA sample metadata

Explore the IMAP-PART 02 interactive snakemake report (if available) here.

IMAP-PART 03

Downloading SRA FastQ reads using fasterq-dump

Explore the IMAP-PART 03 interactive snakemake report (if available) here.

IMAP-PART 04

Quality Control of Sequencing Reads

Explore the IMAP-PART 04 interactive snakemake report (if available) here.

IMAP-PART 05

Microbial profiling with MOTHUR pipeline

Explore the IMAP-PART 05 interactive snakemake report (if available) here.

IMAP-PART 06

Microbial profiling with QIIME2 pipeline

Explore the IMAP-PART 06 interactive snakemake report (if available) here.

IMAP-PART 07

Microbial & functional profiling with BIOBAKERY pipelines

Explore the IMAP-PART 07 interactive snakemake report (if available) here.

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Related work

Repo	Description	Status
IMAP-GLIMPSE	IMAP project overview	In-progress
IMAP-PART 01	Software requirement for microbiome data analysis with Snakemake workflows	In-progress
IMAP-PART 02	Downloading and exploring microbiome sample metadata from SRA Database	In-progress
IMAP-PART 03	Downloading and filtering microbiome sequencing data from SRA database	In-progress
IMAP-PART 04	Quality Control of Microbiome Next Generation Sequencing Reads	In-progress
IMAP-PART 05	Microbial profiling using Mothur pipeline with Snakemake workflows	In-progress
IMAP-PART 06	Microbial profiling using Qiime2 pipeline with Snakemake workflows	In-progress
IMAP-PART 07	Microbial & Functional profiling using Biobakery pipelines with Snakemake workflows	In-progress
IMAP-SUMMARY	Summary of Snakemake workflows for microbiome data analysis	In-progress

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Multi-Omics data analysis

…BRIEF INTRO IN PROGRESS…

Citation

Please consider citing the iMAP article^[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.

References

[1]

Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4

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Appendix

Project main tree

.
├── LICENSE
├── README.md
├── config
│   └── config.yml
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── images
│   ├── bioinformatics.png
│   ├── bkgd.png
│   ├── imap.png
│   ├── imap_part01.svg
│   ├── imap_part02.svg
│   ├── imap_part03.svg
│   ├── imap_part04.svg
│   ├── imap_part05.svg
│   ├── imap_part06.svg
│   ├── imap_part07.svg
│   ├── rulegraph.png
│   └── smkreport
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   └── references.bib
├── report.html
├── results
│   └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    │   ├── mothur.yml
    │   └── qiime220232.yml
    ├── report
    │   ├── biobakery.rst
    │   ├── imap.rst
    │   ├── mothur.rst
    │   ├── qiime2.rst
    │   ├── readqc.rst
    │   ├── rsmkrpt.rst
    │   ├── software.rst
    │   ├── sracache.rst
    │   ├── srametadata.rst
    │   ├── srareads.rst
    │   └── workflow.rst
    ├── rules
    │   ├── render_index.smk
    │   ├── report.smk
    │   └── rules_dag.smk
    └── scripts
        ├── README.md
        ├── files4smk_report.sh
        ├── render.R
        ├── rules_dag.sh
        ├── smk_html_report.sh
        └── tree.sh

12 directories, 48 files

Troubleshooting of FAQs

1. Question
Answer
2. Question
Answer

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Last updated on March 26, 2023.
Github_Repo: https://github.com/tmbuza/imap-snakemake-workflows.
Repo compiled and maintained by: Teresia Mrema-Buza.